title: AGI881_P1_F10_S70, Smart-seq2 (multi-omics)

data_processing:
We processed Smart-seq2 data from raw reads to gene expression matrices as previously described in Neftel et al, 2019. We used bcl2fastq to generate demultiplexed FASTQ files, and aligned the resulting paired-end scRNA-seq reads to the reference transcriptome using Bowtie (v0.12.7). Statistical analysis was done using R version 4.0.1. We merged the gene expression levels which were calculated by RSEM48 for MGH170 and MGH229 with the ones calculated for the reference samples from Tirosh 2016 (downloaded from https://singlecell.broadinstitute.org/single_cell). Analysis was done mainly using the R package scandal which is freely available at https://github.com/dravishays/scandal.  Gene expression levels were quantified as TPM (transcript-per-million reads).
Assembly: GRCh38 for Homo sapiens, mm10 for Mus musculus
Supplementary files format and content: tsv

source_name: Mouse cell line single cell, IDHmutant mouse glioma cell

extract_protocol:
Fresh specimens were mechanically dissociated with a disposable, sterile scalpel and further enzymatically dissociated into single cell suspensions using the enzymatic brain dissociation kit (papain-based) from Miltenyi Biotec as previously reported. Tumor cells were blocked in 1% bovine serum albumin in phosphate-buffered saline solution (1% BSA / PBS). Cell suspensions were subsequently stained for flow cytometry for 30 min at 4 °C using antibodies specific for CD45 [REA747]-VioBlue and CD3 [BW264/56]-PE from Miltenyi Biotec. Cells were washed with cold PBS, and then incubated for 15 min in 1.5 mL of 1% BSA / PBS containing 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies). Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter; CD3-PE, 585/42 filter), 640nm (TO-PRO-3, 670/14 filter), and 405 nm (CD45-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3. We sorted individual, viable, CD45+CD3- and CD45+CD3+ immune, and CD45- non-immune single cells into 96-well plates containing cold TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80 °C prior to whole transcriptome amplification, library preparation and sequencing. Frozen tumor tissue (approximately 5mm x 5mm x 5mm) was placed into a well of a 6-well plate (Corning, Cat. No. CLS3516-50EA) containing 1 ml of CST buffer and processed on ice. Tumor tissue was chopped for 10 minutes using Noyes Spring Scissors (Fine Science Tools, Cat. No. 15514-12). The sample was then filtered through a 40 um cell strainer (Fisher Scientific, Cat. No. 22363547) and the well and filter were washed with an additional 1 ml of CST buffer. The total volume was then brought up to 5 ml with 3 ml of ST buffer and the sample was centrifuged in a 15 ml conical tube at 4°C for 5 minutes at 500 g. The supernatant was removed and the pellet was resuspended in 100 ul ST buffer. The sample was then filtered through a 35 um cell strainer (Falcon, Cat. No. 352235). Nuclei suspension was counted using disposable C-Chip Hemocytometers (INCYTO, Cat. No. DHCN012). Single-nuclei were loaded on 10x genomics or stained by Ruby (ThermoFisher, V10309) and sorted into 96 well plates. IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks.  The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and  640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
RNA from single cells or single nucleus was first purified with Agencourt RNAClean XP beads (Beckman Coulter). B65Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli 2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 768 cells with unique barcodes were combined and sequenced using a NextSeq sequencer (Illumina). Multi-omics library (DNA methylome and transcriptome) was generated based on the Smart-RRBS protocol (Chaligne et al, 2021).

tag: treatment (idhi)

value: Yes


title: A253 cells, sgRNA tomato_2, rep2

status: Public on May 01 2024

type: SRA

city: Madrid

first: Ana

last: Sastre-Perona

state: Madrid

address: Calle Paseo de la Castellana 261, INGEMM, Laboratorio de Epigenética, Hospital Universitario La Paz

country: Spain

institute: IdiPAZ

library_source: transcriptomic

data_processing:
Mapping was done using HISAT2
StringTie was used for transcriptome assembly
Deseq was used to identify differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-delimited tex file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Salivary gland

growth_protocol: A253 control or know-out cells were grown in DMEM supplemented with 10% FBS and humidified atmosphenre at 5% CO2 at 37C

extract_protocol:
total RNA was extracted using Trizol and the microprep RNA extraction kit, Zymo
RNA libraries for RNA-seq were prepared using  the llumina® Stranded mRNA Prep and following the manufacture's instructions

tag: tissue

value: Salivary gland

tag: cell line

tag: cell type

value: Salivary gland SCC

tag: genotype

value: sgRNA control


title: AGI881_P1_F09_S69, Smart-seq2 (multi-omics)

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

country: USA

institute: Massachusetts General Hospital

description: Smartseq2_mouse_multiomics_processed_TPM.tsv

molecule: polyA RNA

organism: Mus musculus

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: A253 cells, sgRNA SOX2, rep1

value: SOX2 KO


title: bLR_RatL08_C2_NACC__NIL_SD

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

data_processing:
Within the MBNI Analysis Hub (“Ahub”: https://ahub.mbni.org) pipeline, RNA-Seq data was aligned using the STAR algorithm (2.7.0f, Encode parameter: unique hit only) to genome assembly Rnor6
Reads were summarized into counts per transcript using featureCounts (v1.6.4) and Ensembl 96 annotation.
Primary quality control: Within the Ahub pipeline, principal components analysis was used to identify extreme outlier samples, which were presumed to reflect unknown sources of technical variation (NACC: 2 samples, HC: 6 samples). These samples did not represent any particular treatment group or processing batch and were removed before further analysis was performed.
Secondary quality control and normalization was performed in Rstudio (v.1.0.153, R v. 3.4.1) for the NACC and HC datasets independently. Only one NACC sample was removed at this stage due to a notably low distribution of log2 counts per million (cpm).
Assembly: Rnor6
Supplementary files format and content: The processed data files are tab-delimited text files that include the read counts per transcript (Rnor6 with Ensembl 96 annotation) for each sample that survived the first level of quality control. There is a separate file for the Nucleus Accumbens samples (NAcc_remove2samples_gene_featureCounts_counts.txt) and Hippocampal samples (Hippocampus_remove6samples_gene_featureCounts_counts.txt) because they were processed in separate batches.

organism: Rattus norvegicus

source_name: nucleus accumbens (NACC)

growth_protocol: The male bred Low-Responder (bLR) Sprague-Dawley rats used in the RNA-Seq experiment were from the University of Michigan MBNI colony (generations F49, F53, F56). Litters were culled on postnatal day 1 (P1) to even sex ratios (minimum litter size: 3M/3F, maximum: 6M/6F). Animals were housed on a 12:12 hour light:dark cycle (lights on: 7am) with ad libitum access to water and food. Litters were weaned at P21 and males were pair- or triple-housed with littermates.

extract_protocol:
Tissue and blood collection: On P68, animals habituated to a new room (>30 minutes), then were removed to the sacrifice room and immediately decapitated without anaesthesia. Trunk blood was collected in EDTA tubes and placed onto ice before centrifugation (3000 rpm, 4oC) for 10 minutes. Plasma supernatant was stored at -80oC. Brains were removed within 2 minutes of death, flash-frozen (-30oC), and stored at -80oC.  All brains were hemi-sected (groups counter-balanced by side), and one half dissected within a cryostat (-20oC); the NAcc (+1.5mm to +1mm Anterior-Posterior [46]) was extracted by 2mm hole-punch, and whole dorsal HC (-3mm to -4mm Anterior-Posterior [46]) extracted using dissection tools.   RNA extraction: Nucleotides were extracted from NACC and HC tissue using Qiagen AllPrep DNA RNA miRNA Universal Kit 50. Extracted RNA was evaluated for total concentration and quality using a Nanodrop spectrophotometer (concentration range: 285-432 ng/ul, 260/280 ratio range: 1.61-1.80).
Samples were processed by the University of Michigan DNA Sequencing Core (https://brcf.medicine.umich.edu/cores/dna-sequencing/). RNA integrity (RIN) was assessed using the TapeStation automated sample processing system (Agilent, Santa Clara, CA). Samples with RINs<8 were excluded. A DNA library targeting polyadenylated transcripts was constructed for each sample (100ng total RNA) with the KAPA hyper mRNA stranded library prep kit (Roche, catalogue# KK8581) in a 12-cycle PCR. Final cDNA libraries were checked for quality by TapeStation (Agilent) and qPCR using Kapa’s library quantification kit for Illumina Sequencing platforms (catalogue# KK4835, Kapa Biosystems, Wilmington MA).

treatment_protocol: Adolescent Enrichment: At postnatal day 35 a subset of animals was assigned to a group to receive Social and Environmental Enrichment (EE). Enriched cages consisted of a large (50 x 40 x 50cm) cage with three separate levels connected by mesh ramps, and contained various other objects that were added to the cage and moved around over the duration of enrichment. EE groups spent an hour a day in these cages, 5 days a week from P35 to P60. All animals from one litter were placed into the same EE cage such that the number of animals present during each session was between 4 and 6, depending on litter size. The comparison group (NIL) received standard housing from P35-P60.  Repeated social stress:  From P61-64, the experimental bHR/bLR rats were each introduced individually to a Long-Evans aggressor’s cage to experience a daily 15-minute social stress episode. The bHR/bLR intruder could move freely throughout the cage until an aggressive interaction (pinning). Intruders were then placed into a protective wire mesh container (10x10x15cm) within the Long-Evans cage for the remainder of the trial.  Each day, each bLR/bHR intruder was exposed to a different Long-Evans aggressor. Any rat that sustained physical wounds during social defeat was excluded from the study. Experimental bHR/bLR rats that were in the no defeat group (“NIL”) were placed in a clean, empty novel cage within the same testing room and allowed to move freely for the 15-minute period.   Behavioural testing: On P65-66, experimental animals underwent a social interaction test consisting of two 5-minute trials on consecutive days (Day 1: habituation, Day 2: testing). The testing arena was a white Plexiglass open field (100x100cm). The bHR/bLR rats were placed into the centre of the testing field on both days. On Day 2, there was a caged novel stimulus male Long-Evans rat (“target”) present, with zones of the open field predefined as target, interaction, and social avoidance zones. A video tracking system (Ethovision XT 11.5, Noldus Information Technology) calculated the percent time the bHR/bLR rats spent in each zone. On P67, animals underwent the Elevated Plus Maze (EPM). The EPM consists of four intersecting black Plexiglass arms (45cmx12cm) shaped like a cross, elevated 70cm from the floor. Two opposite arms are enclosed (45cm walls) and two remain open; at the intersection a square platform (12x12cm) allows access to all arms. During the five-minute test, the room was dimly lit (40 lux) and animals’ behaviour monitored using a video tracking system (Ethovision XT 11.5, Noldus Information Technology ) that recorded latency to enter the open arm, the amount of time spent in the arms and centre square.

tag: rat

tag: hemisphere

value: left

tag: animal strain

value: bred Low Responder (bLR)

tag: social defeat stress

value: social defeat stress (SD)

tag: adolescent environmental enrichment

value: standard housing (NIL)

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma corticosterone (pg/ml)

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control

value: Good


title: A253 cells, sgRNA tomato_2, rep1

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: A253 cells, sgRNA DUSP1 clon10, rep2

value: DUSP1 KO clon 10


title: AGI881_P1_F07_S67, Smart-seq2 (multi-omics)

tag: treatment (idhi)


title: A253 cells, sgRNA DUSP1 clon10, rep1


title: A253 cells, sgRNA DUSP1 clon1, rep2

value: DUSP1 KO clon 1


title: bLR_RatL08_C1_NACC__NIL_SD

tag: rat

tag: hemisphere

value: right

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection


title: A253 cells, sgRNA DUSP1 clon1, rep1


title: bLR_RatL08_B2_NACC__NIL_SD

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: AGI881_P1_F05_S65, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: A253 cells, sgRNA tomato, rep2

tag: cell line

tag: cell type

tag: genotype


title: AGI881_P1_F06_S66, Smart-seq2 (multi-omics)


title: A253 cells, sgRNA tomato, rep1


title: bLR_RatL08_B1_NACC__NIL_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: plasma corticosterone (pg/ml)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: AGI881_P1_F04_S64, Smart-seq2 (multi-omics)


title: bLR_RatL08_A2_NACC__NIL_SD

tag: family

tag: date of sacrifice

tag: date of dissection

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: Biopsy IL15.CAR 15.CAR CAR-PCR Patient 5

city: Houston

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

description:
ProductsBx_integrated.metadata.csv
ProductsBx_integrated.rawcounts.csv
ProductsBx_integrated.scaledcounts.csv
ProductsBx_integrated.umapcoordinates.csv

library_source: other

data_processing:
FASTQ files were analyzed with the 10× Genomics Cell Ranger (v7.1.0) software pipeline, including demultiplexing and read alignment to the CAR-augmented human reference genome GRCh38.p13 to detect endogenous and CAR RNAs.
Genes detected in less than 10 cells, cells with fewer than 200 profiled genes, and more than 10% of mitochondrial Raw unique molecular identifiers (UMIs) were removed to exclude low-quality or dying cells. Cells with more than 7,000 genes were excluded. Doublets were identified using DoubletFinder.
UMI counts were Log Normalized with a scale factor of 10,000. Feature variance was then calculated, and the top 2,000 highly variable features (genes) were retained and scaled (linear transformation). CAR+ cells in pre-infusion product samples were integrated using the harmony package.
When clustering CAR T product samples, we performed principal component analysis (PCA) on the scaled data and unsupervised Louvain clustering analysis with a resolution of 0.5. A total of 12 clusters were identified from 24 pre-infusion product samples. Cells in each cluster were projected onto a two-dimensional UMAP.
B cells, red blood cells, and monocytes were filtered out by removing cells where HBB, CD79A, MS4A1, CD19, CD22, CD14, and MS4A7 reads were > 0.
Assembly: hg38
Supplementary files format and content: Products_integrated.metadata.csv, contains cells metadata from the integrated Product samples
Supplementary files format and content: Products_integrated.rawcounts.csv, contains cells raw counts from the integrated Product samples
Supplementary files format and content: Products_integrated.scaledcounts.csv, contains cells scaled data from the integrated Product samples
Supplementary files format and content: Products_integrated.umapcoordinates.csv, contains the UMAP coordinates from the integrated Product samples
Supplementary files format and content: ProductsPB_integrated.metadata.csv, contains cells metadata from the integrated Product and PB samples
Supplementary files format and content: ProductsPB_integrated.rawcounts.csv, contains cells raw counts from the integrated Product and PB samples
Supplementary files format and content: ProductsPB_integrated.scaledcounts.csv, contains cells scaled data from the integrated Product and PB samples
Supplementary files format and content: ProductsPB_integrated.umapcoordinates.csv, contains the UMAP coordinates from the integrated Product and PB samples
Supplementary files format and content: ProductsxBx_integrated.metadata.csv, contains cells metadata from the integrated Product and Bx samples
Supplementary files format and content: ProductsBx_integrated.rawcounts.csv, contains cells raw counts from the integrated Product and Bx samples
Supplementary files format and content: ProductsBx_integrated.scaledcounts.csv, contains cells scaled data from the integrated Product and Bx samples
Supplementary files format and content: ProductsBx_integrated.umapcoordinates.csv, contains the UMAP coordinates from the integrated Product and Bx samples

molecule: other

source_name: CAR-T cells

extract_protocol:
Cells were dissociated, and scRNA-seq libraries were prepared according to Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 kit (10x Genomics).
scRNA-seq libraries were prepared according to Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (10x Genomics). CAR transcript were amplified by PCR. Libraries were sequenced on NovaSeq6000.

tag: cell type

value: CAR-T cells

tag: construct

value: CAR + IL15


title: bLR_RatL08_A1_NACC__NIL_SD

tag: rat

tag: hemisphere

tag: animal strain

tag: social defeat stress

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: Biopsy IL15.CAR 15.CAR CAR-PCR Patient 2


title: Biopsy IL15.CAR 15.CAR CAR-PCR Patient 4


title: AGI881_P1_F02_S62, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: PBMCs CAR CAR CAR-PCR Patient 4

description:
ProductsPB_integrated.metadata.csv
ProductsPB_integrated.rawcounts.csv
ProductsPB_integrated.scaledcounts.csv
ProductsPB_integrated.umapcoordinates.csv

value: CAR


title: AGI881_P1_F03_S63, Smart-seq2 (multi-omics)

value: Yes


title: PBMCs CAR CAR CAR-PCR Patient 5


title: PBMCs CAR DL1.CAR CAR-PCR Patient 5


title: AGI881_P1_F01_S61, Smart-seq2 (multi-omics)


title: bLR_RatL09_B3_NACC__NIL_NIL

value: no social defeat stress (NIL)

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: date of dissection

tag: plasma corticosterone (pg/ml)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: PBMCs CAR DL1.CAR CAR-PCR Patient 1

tag: cell type

tag: construct


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 12


title: AGI881_P1_E12_S60, Smart-seq2 (multi-omics)


title: bLR_RatL09_B2_NACC__NIL_NIL

tag: rat

tag: hemisphere

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 11


title: bLR_RatL09_B1_NACC__NIL_NIL

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 9


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 7


title: bLR_RatL09_A2_NACC__NIL_NIL

tag: family

tag: date of sacrifice

tag: date of dissection

tag: plasma corticosterone (pg/ml)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: AGI881_P1_E10_S58, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 8

tag: cell type

tag: construct


title: AGI881_P1_E09_S57, Smart-seq2 (multi-omics)


title: bLR_RatL09_A1_NACC__NIL_NIL

tag: rat

tag: hemisphere

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: AGI881_P1_E08_S56, Smart-seq2 (multi-omics)


title: bLR_RatL10_A3_NACC__NIL_NIL

tag: animal strain

tag: social defeat stress

tag: adolescent environmental enrichment

tag: generation

tag: family

tag: date of sacrifice

tag: social interaction (percent time in interaction zone during social interaction test)

tag: aggressive behavior (percent time on top of stimulus animal in social interaction test)


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 4

tag: cell type

tag: construct


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 1


title: bLR_RatL10_A2_NACC__NIL_NIL

tag: rat

tag: hemisphere

tag: date of dissection

tag: plasma corticosterone (pg/ml)

tag: exploratory behavior vs. anxiety-like behavior (percent time in the anxiogenic open arms of the epm)

tag: failed quality_control


title: AGI881_P1_E07_S55, Smart-seq2 (multi-omics)

tag: tissue

tag: treatment (idhi)


title: Biopsy IL15.CAR 15.CAR mRNA Patient 10

library_source: transcriptomic single cell


title: Biopsy IL15.CAR 15.CAR mRNA Patient 12


title: bLR_RatL10_A1_NACC__NIL_NIL

tag: animal strain

tag: social defeat stress

tag: date of rna extraction

tag: rna concentration

tag: rna 260 280 ratio

tag: plasma testosterone (pg/ml)

tag: distance traveled (open field habituation)

tag: social avoidance (percent time in avoidance zone during social interaction test)


title: Biopsy IL15.CAR 15.CAR mRNA Patient 8

tag: cell type

tag: construct


title: Patid22

city: COLUMBUS

first: Deedra

middle: R

last: Nicolet

state: OH

address: 1800 Cannon Drive, Rm 1250H

department: CCC

institute: The Ohio State University

data_processing:
RNA-seq data were processed using the EnFusion ensemble approach of seven fusion detection algorithms
Transcripts per million (TPM) values were generated from paired-end RNA sequence data using Salmon with bootstrapping set to 100
Assembly: Homo sapiens GRCh38.p12
Supplementary files format and content: Salmon TPM

source_name: BM/pB

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq Stranded Total with Rebo Zero Gold library preparation kit following manufacturer's protocols.
Tumor derived RNA was subjected to 0.8x SPRI beadcleanup and size selection prior to DNase treatment and ribodepletion prior to using the NEBNext Ultra II Directional kit preparation. The library was constructed for whole transcriptome sequencing (RNA-seq). Paired-end 151-bp reads were generated on the Illumina NovaSeq (Illumina, Inc.)

value: BM/pB

value: mononuclear leukocytes

tag: treatment

value: cytotoxic induction therapy with cytarabine/daunorubicin


title: AGI881_P1_E06_S54, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: Biopsy IL15.CAR 15.CAR mRNA Patient 9


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 10


title: Biopsy IL15.CAR 15.CAR mRNA Patient 7


title: AGI881_P1_E11_S59, Smart-seq2 (multi-omics)


title: AGI881_P1_E05_S53, Smart-seq2 (multi-omics)


title: Biopsy IL15.CAR 15.CAR mRNA Patient 5


title: Biopsy IL15.CAR 15.CAR mRNA Patient 4


title: AGI881_P1_E04_S52, Smart-seq2 (multi-omics)


title: PBMCs IL15.CAR 15.CAR CAR-PCR Patient 5


title: Patid21


title: PBMCs CAR CAR mRNA Patient 5


title: AGI881_P1_E03_S51, Smart-seq2 (multi-omics)


title: Patid20


title: PBMCs CAR CAR mRNA Patient 4


title: PBMCs CAR DL1.CAR mRNA Patient 5


title: Patid19


title: AGI881_P1_E02_S50, Smart-seq2 (multi-omics)


title: PBMCs CAR CAR mRNA Patient 1


title: Patid18


title: PBMCs IL15.CAR 15.CAR mRNA Patient 11


title: AGI881_P1_D12_S48, Smart-seq2 (multi-omics)


title: PBMCs IL15.CAR 15.CAR mRNA Patient 10


title: Patid17


title: PBMCs IL15.CAR 15.CAR mRNA Patient 9


title: AGI881_P1_D11_S47, Smart-seq2 (multi-omics)


title: PBMCs IL15.CAR 15.CAR mRNA Patient 8


title: Patid16


title: PBMCs IL15.CAR 15.CAR mRNA Patient 4


title: Biopsy IL15.CAR 15.CAR mRNA Patient 2


title: PBMCs IL15.CAR 15.CAR mRNA Patient 7


title: AGI881_P1_D10_S46, Smart-seq2 (multi-omics)


title: Patid15


title: PBMCs IL15.CAR 15.CAR mRNA Patient 1


title: AGI881_P1_D09_S45, Smart-seq2 (multi-omics)


title: PBMCs IL15.CAR 15.CAR mRNA Patient 5


title: Patid14


title: AGI881_P1_D08_S44, Smart-seq2 (multi-omics)


title: Patid13


title: Product CAR CAR mRNA Patient 5

description:
Products_integrated.metadata.csv
Products_integrated.rawcounts.csv
Products_integrated.scaledcounts.csv
Products_integrated.umapcoordinates.csv


title: Product CAR CAR mRNA Patient 4


title: Product CAR DL1.CAR mRNA Patient 6


title: Patid12


title: Product CAR CAR mRNA Patient 6


title: AGI881_P1_D06_S42, Smart-seq2 (multi-omics)


title: PBMCs IL15.CAR 15.CAR mRNA Patient 12


title: AGI881_P1_D04_S40, Smart-seq2 (multi-omics)


title: Patid11


title: Product CAR CAR mRNA Patient 3


title: Product CAR DL1.CAR mRNA Patient 4


title: AGI881_P1_D03_S39, Smart-seq2 (multi-omics)


title: Patid10


title: Product CAR CAR mRNA Patient 1


title: AGI881_P1_D01_S37, Smart-seq2 (multi-omics)


title: Product CAR DL1.CAR mRNA Patient 3


title: Patid09


title: AGI881_P1_C10_S34, Smart-seq2 (multi-omics)


title: Product CAR DL1.CAR mRNA Patient 1


title: Product CAR DL1.CAR mRNA Patient 2


title: Product IL15.CAR 15.CAR mRNA Patient 12


title: Patid08


title: Patid07


title: Product IL15.CAR 15.CAR mRNA Patient 9


title: Product IL15.CAR 15.CAR mRNA Patient 11


title: Product CAR DL1.CAR mRNA Patient 5


title: Patid06


title: AGI881_P1_C08_S32, Smart-seq2 (multi-omics)


title: Product IL15.CAR 15.CAR mRNA Patient 10


title: Product IL15.CAR 15.CAR mRNA Patient 8


title: AGI881_P1_C07_S31, Smart-seq2 (multi-omics)


title: Product IL15.CAR 15.CAR mRNA Patient 5


title: Product CAR CAR mRNA Patient 2


title: Patid04


title: AGI881_P1_C05_S29, Smart-seq2 (multi-omics)


title: AGI881_P1_C04_S28, Smart-seq2 (multi-omics)


title: Product IL15.CAR 15.CAR mRNA Patient 3


title: Product IL15.CAR 15.CAR mRNA Patient 4


title: Product IL15.CAR 15.CAR mRNA Patient 6


title: Product IL15.CAR 15.CAR mRNA Patient 2


title: AGI881_P1_C03_S27, Smart-seq2 (multi-omics)


title: AGI881_P1_C09_S33, Smart-seq2 (multi-omics)


title: Product IL15.CAR 15.CAR mRNA Patient 1


title: Patid02


title: CTRL2

city: Callaghan

first: Ting

last: La

state: NSW

address: University Drive

country: Australia

institute: UON

data_processing:
cell ranger(version 5.0.0; 10 × Genomics, Pleasanton, CA) was used to process the raw data
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Parathyroid

extract_protocol:
the cells were resuspended in calcium- and magnesium-free PBS containing 0.04% BSA, followed by centrifugation at 300g for 5 min. The cells were then resuspended in 1mL of ice-cold red blood cell lysis buffer.and incubated at 4 °C for 10 min, followed by the addition of 10 ml of ice-cold PBS and centrifugation at 300g for 10 min. After resuspension, the sample was filtered with a 40-μm cell strainer. Cell viability was then determined using Trypan Blue staining with an automated cell counter.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Parathyroid

tag: cell line

value: parathyroid cell

tag: genotype

value: total RNA


title: CTRL3

value: para-carcinoma tissue


title: Patid01


title: Product IL15.CAR 15.CAR mRNA Patient 7


title: CTRL1


title: AGI881_P1_C01_S25, Smart-seq2 (multi-omics)


title: HUDEP-2 TL20804:TL20805 transfected, clone 124, rep 3

city: Seattle

first: Jeff

last: Vierstra

state: WA

address: 2211 Elliot Ave

institute: Altius Institute for Biomedical Sciences

data_processing:
Basecalling, RTA v3.4.4
Alignments to GRCh38, star v2.4.2a
Annotation, cufflinks v2.2.1, GENCODE v25
Subread, featureCounts v1.5.1
Assembly: GRCh38
Supplementary files format and content: featureCounts gene counts per sample as gzipped tab-delimited matrix

growth_protocol: HUDEP-2 were maintained in Iscove's modified Dulbecco's medium (IMDM) supplemented with 330 μg/mL human holo-transferrin (Sigma), 10 μg/mL recombinant human insulin (Sigma), 2 IU/mL heparin (Sigma), 5% human AB plasma (obtained from Bloodworks Northwest, Seattle, WA), 3 IU/mL EPO, 100 ng/mL SCF, 1 μg/mL doxycycline (Sigma), and 100 units/ml penicillin/streptomycin.

extract_protocol:
Approximately 200,000 cells were collected per culture and total RNA was isolated using QIAGEN RNeasy kit per manufacturer's instructions
RNA library was constructed using the Illumina RNA TruSeq Stranded tRNA with Ribo-Zero Globin

value: human erythroid progenitor

value: PVT1 DHS knockout

value: untreated


title: Patid05


title: HUDEP-2 TL20804:TL20805 transfected, clone 124, rep 2


title: CLL cells from patient 2 cultured on 3T40 for 48 hours in presence of 100 nM Dasatinib

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

data_processing:
Sequence quality was assessed with FastQC, raw FASTq files were aligned with hisat2.1.0
Counts file is output of hisat
Assembly: GRCh38/hg38
Supplementary files format and content: raw counts in comma-delimited format

source_name: Blood PBMCs

extract_protocol:
Total RNA was extracted with the Qiagen Mini kit
KAPA mRNA Hyperprep
mRNA sequencing on Illumina HiSeq 4000

value: Blood PBMCs

value: B cells

tag: Sex

value: Female

tag: mutation status

value: Unmutated

tag: time

value: 48 hours


title: CLL cells from patient 4 cultured on 3T40 for 48 hours in presence of 100 nM Dasatinib

tag: tissue

value: Mutated


title: AGI881_P1_B12_S24, Smart-seq2 (multi-omics)

tag: treatment (idhi)

value: Yes


title: AGI881_P1_B09_S21, Smart-seq2 (multi-omics)


title: IRI_3，kidney,H4K12la

city: Guangzhou

first: yating

last: wang

state: Guangdong

address: 58th Zhongshan Road II  The First Affiliated Hospital ,Sun Yat-Sen University

department: Department of Nephrology

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

library_source: genomic

data_processing:
Index of the reference genome was built using Bowtie2 and clean reads were aligned to the reference genome. All peak calling was performed with MACS2 using ‘macs2 -q 0.05 --call-summits --nomodel--shift -100 --extsize 200 --keep-dup all’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering. The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene.
Peak Annotator was used to identify the nearest TSS of every peak and the distance distribution between peaks and TSS was shown. Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Bigwig data of each sample
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: kidney

extract_protocol:
CUT &Tag assay was conducted with Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (TD901, Vazyme) according to the manufacturer’s instructions.
The DNA fragment samples were isolated and amplified for library construction based on the manufacturer’s instructions (TD202, Vazyme ).

value: kidney

value: IRI


title: IRI_4，kidney,H4K12la


title: CLL cells from patient 1 cultured on 3T40 for 48 hours in presence of 100 nM Dasatinib

value: Male


title: AGI881_P1_B08_S20, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: HUDEP-2 mock transfected, clone 62 rep 3

value: WT


title: HUDEP-2 TL20804:TL20805 transfected, clone 124, rep 1


title: ATAC-Seq, shBRD9-81-C

city: Boston

first: Swati

last: Garg

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
shBRD9 rep C
KD12.merged_peaks.bed.gz

data_processing:
Sequence reads were trimmed for adapter sequences and poor quality nucleotides using Trimmomatic v.0.38
Trimmed reads were aligned to reference genome hg38 using bowtie2
Samtools 1.9 was used to filter aligned reads
Picard 2.18.26 was used to remove optical duplicates, mtDNA and unplaced contigs were removed prior to peak calling
MACS2 2.1.2 was used for peak calling. Valid peaks from each group or condition were then merged and peaks called in at least 66% of samples were kept for downstream analyses
Assembly: hg38
Supplementary files format and content: bed files merged peaks

source_name: Blood

growth_protocol: Cells were placed in CD34 media containing IMDM+20%BIT and 100ng/mL rH-SCF and FL, and 50ng/mL TPO, supplemented with 100microM 2-mercaptoethanol and genatmicin/ciprofloxacin

extract_protocol:
nuclei were treated with Tn5 enzyme
Tagmented DNA was barcoded with Nextera Index kit v2

treatment_protocol: High titer lentivirus infection was carried out at MOI 30 in presence of 10 microg/mL protamine sulphate

value: Blood

value: CD34 HSPC

value: BRD9 knockdown

value: Lentiviral infection/FACS sort


title: IRI_1，kidney,H4K12la


title: Patid03

value: BM/pB

value: mononuclear leukocytes

value: cytotoxic induction therapy with cytarabine/daunorubicin


title: AGI881_P1_B07_S19, Smart-seq2 (multi-omics)


title: HUDEP-2 mock transfected, clone 62 rep 2

value: human erythroid progenitor

value: untreated


title: ATAC-Seq, shBRD9-81-B

description:
shBRD9 rep B
KD12.merged_peaks.bed.gz


title: AGI881_P1_B06_S18, Smart-seq2 (multi-omics)


title: HUDEP-2 mock transfected, clone 62 rep 1


title: AGI881_P1_C02_S26, Smart-seq2 (multi-omics)


title: ATAC-Seq, shBRD9-33-C

description:
shBRD9 rep C
KD12.merged_peaks.bed.gz


title: Sham_1，kidney,H4K12la

value: Sham


title: HUDEP-2 TL20804:TL20805 transfected, clone 124, rep 3, DNase-I 90U/mL

data_processing:
Basecalling, RTA v3.4.4
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.3
Read density, Bedops v2.4.15
Peak calling, Hotspot2 v2.1.1
Assembly: GRCh38
Supplementary files format and content: Normalized DNaseI density bigWig files
Library strategy: DNaseI-seq

extract_protocol:
Nuclei from 100,000-200,000 cells were extracted in the presence of 0.04% de-ionized IGEPAL CA-630 incubated at 4 ºC for 10 min. Nuclei were treated with a gradient of DNase I solution (40 IU to 100 IU of DNase I) for 3 min at 37 ºC. DNase I digestion was quenched by adding an equal volume of 5X Stop buffer and 20μL RNase A (Sigma, R4642) followed by incubation at 37 ºC for 60min. After incubation, 1μL of Proteinase K (Sigma, P4850) was added and the reactions were incubated at 50 ºC for 60min. Digested genomic DNA was visualized on 1.2% agarose gen and the fragment size profile was generated using the Fragment Analyzer (Advanced Analytical). Prior to genomic library generation, fragments were subjected to size selection with large fragment depletion by magnetic bead separation. Fragment size distribution and concentration of the fractionated sample was measured with Fragment Analyzer (Advanced Analytical).
Illumina compatible, double-stranded DNA library libraries from the size fractionated samples were constructed using the ThruPLEX DNA-seq Kit (Takara Bio) according to manufacturer’s instructions.

value: human erythroid progenitors

value: PVT1-DHS knockout


title: AGI881_P1_B05_S17, Smart-seq2 (multi-omics)

value: Yes


title: ATAC-Seq, shBRD9-81-A

description:
shBRD9 rep A
KD12.merged_peaks.bed.gz


title: AGI881_P1_B04_S16, Smart-seq2 (multi-omics)


title: ATAC-Seq, shBRD9-33-B

description:
shBRD9 rep B
KD12.merged_peaks.bed.gz


title: HUDEP-2 TL17275:TL17276 & TL17287:TL17288 transfected, clone 24, rep 5, Dnase-I 120 U/mL

value: PPARA-DHS knockout


title: Pfkfb3ΔPTC3, Kidney, IRI day14

data_processing:
Differential expression analysis between IRI kidney with Pfkfb3ΔPTC  or Pfkfb3WT was performed using the DESeq2 R package (1.16.1) and padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text file  include raw counts for each sample

extract_protocol:
Total RNA isolated from kidney tissues and quantitative to 500 ng per sample was used as input material for the RNA sequence.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: The IRI mouse model was anesthetized followed by conducting clamp bilateral renal arteries for 30 min.

value: kidney

value: PFKFB3 CKO

value: IRI day14


title: AGI881_P1_B03_S15, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: IRI_2，kidney,H4K12la

value: IRI


title: Pfkfb3ΔPTC2, Kidney, IRI day14


title: AGI881_P1_B01_S13, Smart-seq2 (multi-omics)


title: ATAC-Seq, shNT-C

description:
control rep C
Control.merged_peaks.bed.gz

value: Blood

value: CD34 HSPC

value: WT


title: Pfkfb3ΔPTC1, Kidney, IRI day14


title: AGI881_P1_A12_S12, Smart-seq2 (multi-omics)


title: ATAC-Seq, shNT-B

description:
control rep B
Control.merged_peaks.bed.gz

value: Lentiviral infection/FACS sort


title: Pfkfb3WT3, Kidney, IRI day14

value: PFKFB3 WT


title: RNAseq MDVR Rep3

city: Los Angeles

first: Emmanuelle

last: Hodara

state: CA

address: 1450 Biggy Street

institute: Keck School of Medicine of USC

data_processing:
Samples were aligned to the hg38 with reference annotation GENCODE v39 using STAR (2.7.0).
Only uniquely mapped reads without duplicates were selected usign samtools (version 1.10)
Read counts were assigned to genes using Subread featureCounts.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab delimited files containing gene names and featurecounts

source_name: cell line

growth_protocol: RPMI, 10% fetal bovine serum, 1% Penicillin/Streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA Extraction using Zymo RNA MiniPrep Kit followed by library preparation
NEBNExt Ultra II RNA Library Prep Kit for Illumina (Catalog# E7420, NEB)

treatment_protocol: Grown to 3 days confluence

value: cell line

value: MDVR

value: Human prostate cancer

value: Day 3


title: RNAseq MDVR Rep4


title: Pfkfb3WT2, Kidney, IRI day14


title: AGI881_P1_A09_S9, Smart-seq2 (multi-omics)


title: AGI881_P1_A08_S8, Smart-seq2 (multi-omics)


title: RNAseq MDVR Rep1


title: Sham_2，kidney,H4K12la

value: Sham


title: RNAseq C4-2B Rep4


title: Pfkfb3WT1, Kidney, IRI day14


title: shBRD9-81-C

description: shBRD9 rep C

data_processing:
Sequence reads were trimmed for adapter sequences and poor quality nucleotides using Trimmomatic v.0.36
Trimmed reads were mapped using the STAR aligner v2.5.2b
Unique gene hit counts were calculated using Subread package v.1.5.2
DESeq2
Assembly: Homo sapiens GRCh38
Supplementary files format and content: comma seperated value file contains raw counts per sample

extract_protocol:
RNA was extracted using Qiagen Rneasy kit
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions

value: BRD9 knockdown


title: AGI881_P1_A05_S5, Smart-seq2 (multi-omics)

value: Yes


title: Pfkfb3WT3, Kidney, Sham

value: kidney


title: AGI881_P1_A07_S7, Smart-seq2 (multi-omics)


title: RNAseq C4-2B Rep2


title: shBRD9-81-A

description: shBRD9 rep A


title: Pfkfb3WT2, Kidney, Sham


title: shBRD9-81-B

description: shBRD9 rep B


title: Pfkfb3WT1, Kidney, Sham


title: ATAC-Seq, shBRD9-33-A

description:
shBRD9 rep A
KD12.merged_peaks.bed.gz


title: shBRD9-33-C

description: shBRD9 rep C


title: AGI881_P1_A03_S3, Smart-seq2 (multi-omics)


title: RNAseq MDVR Rep2


title: RNAseq C4-2B Rep1


title: BM_HSC_Rank-ki, rep2

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq2 v2.20.0
Reads were aligned to the mouse reference (mm10) with support of the Ensembl v98 splice sites using the aligner gsnap v2020-12-16.
Uniquely mapped fragments were quantified on Ensembl v98 gene annotation using featureCounts v2.0.1.
Assembly: mm10 (Ensembl v98)
Supplementary files format and content: Tab delimited text files include TPM normalized read counts for each sample.

source_name: Bone marrow

extract_protocol:
HSCs (KSL CD48- CD150+) were FACsorted and RNA was extracted according to the method described by Picelli, S. et al. (DOI: 10.1038/nmeth.2639).
For library preparation 2 µl cDNA was tagmented using the Illumina DNA Prep Kit according to manufacturers instructions.

value: Bone marrow

value: HSCs

value: RankCre-ki

tag: strain

value: female


title: AGI881_P1_A02_S2, Smart-seq2 (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: shBRD9-33-B

description: shBRD9 rep B

value: Blood

value: CD34 HSPC


title: MeRIP (C4-2B dataset) T24R2 Rep 4 RIP (C4-2B dataset)

data_processing:
Samples were aligned to the hg38 with reference annotation GENCODE v39 using STAR (2.7.0).
Only uniquely mapped reads without duplicates were selected usign samtools (version 1.10)
Unique read files were used for peak calling using MACS2 (3.0.0a6) using the callpeaks with the options “-nomodel -extsize100 -gsize300e6”
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig files for visualization
Supplementary files format and content: MACS2 called peaks

extract_protocol:
RNA Extraction using Zymo RNA MiniPrep Kit followed by low-input MeRIP protocol
SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian (Catalog # 634413, Takara-Clontech, Japan)
MeRIP-seq

value: WT

tag: merip antibody

value: anti m6A antibody (NEB, E1610)


title: AGI881_P1_A01_S1, Smart-seq2 (multi-omics)


title: MeRIP (C4-2B dataset) T24R2 Rep 3 RIP (C4-2B dataset)

value: cell line


title: BM_HSC_Rank-ki, rep1


title: shBRD9-33-A

description: shBRD9 rep A

value: Lentiviral infection/FACS sort


title: ATAC-Seq, shNT-A

description:
control rep A
Control.merged_peaks.bed.gz


title: shNT-C

description: control rep C


title: MeRIP (C4-2B dataset) T24R2 Rep 2 RIP (C4-2B dataset)

value: MDVR

value: Human prostate cancer


title: BM_HSC_wt, rep2

value: wild-type


title: DMSO_P1_B12, scRRBS (multi-omics)

description: scRRBS_mouse_multiomics_processed_CpG.tsv

data_processing:
Analysis of single cell DNA methylation data was performed based on the methods detailed in Chaligne et al 2021. After demultiplexing, reads were mapped to the mm10 genome and cells with at least 25,000 CpG sites, 1 million reads and mapping efficiency greater than 30% were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: tsv

extract_protocol:
IdhR132H mouse glioma cells were cultured in the presence of 1 μM AG-881or vehicle (DMSO control) for > 2 weeks.  The treated cells were washed with cold PBS and then stained with 1 uM calcein AM (Life Technologies) and 0.33 uM TO-PRO-3 iodide (Life Technologies) for 30 min at 4°C. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter) and  640nm (TO-PRO-3, 670/14 filter). Side scatter (SSC) width versus forward scatter (FSC) area, and Trigger Pulse Width versus FSC criteria were used to discriminate doublets. Calcein AM positive and TO-PRO-3 negative live cells were sorted into 96 wells containing TCL buffer (QIAGEN) for the single-cell multi-omics experiment.
The single-cell plates for the mouse glioma cells treaded by AG-881 or DMSO were profiled by the joint single-cell RRBS and whole transcriptome amplification (Smart-seq2) protocol. The library preparation and sequencing were performed as previously described (Chaligne et al, 2021). Single enzyme digestion (MspI) was used to enrich CpG dense regions in single-cell RRBS.

value: No


title: DMSO_P1_B05, scRRBS (multi-omics)


title: RNAseq C4-2B Rep3

value: Day 3


title: MeRIP (C4-2B dataset) T24R2 Rep 1 RIP (C4-2B dataset)


title: MeRIP (C4-2B dataset) T24R2 Rep 4 Input

value: Input Ctrl - no antibody


title: IS-caput, Ovch2 KO, rep3

city: Nagoya

first: Daiji

last: Kiyozumi

state: Aichi

address: Furocho, Chikusa-ku

department: Research Institute of Environmental Medicine

country: Japan

institute: Nagoya University

data_processing:
NovaSeq6000 (Illumina) using 101 bp single-ended mode
sequence reads were mapped onto mouse reference genome (mm10) using TopHat ver. 2.1.1
Fragments Per Kilobase of exon per Million mapped reads (FPKM) values for each gene were calculated using Cufflinks ver. 2.2.1
Assembly: mm10
Supplementary files format and content: A Microsoft Excel file including FPKM values for each Sample

source_name: IS-caput epididymis

extract_protocol:
RNA was harvested using TRIzol (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA sample prep kit (Illumina) following manufacturer's protocols.

value: IS-caput epididymis

tag: age

value: no treatment


title: DMSO_P1_B04, scRRBS (multi-omics)


title: BM_HSC_wt, rep1

value: Bone marrow

value: HSCs

value: male


title: shNT-B

description: control rep B

value: Blood


title: shNT-A

description: control rep A

value: CD34 HSPC


title: C1.PFOS_10.4

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p14 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (≥|2.0|-fold and ≤5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Assembly: human genome assembly NCBI GRCh38.p14
Supplementary files format and content: TMM normalized log counts per million (log CPM) values for each Sample

source_name: testes

growth_protocol: Cells were plated in DMEM with 10% FBS and 1% L-glutamine and 1x-Antibiotic/antimycotic

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.

treatment_protocol: (cells) indicated PFOS or vehicle control for 4 days; (mice) dosed with indicated PFAS or vehicle control for 15 days

value: testes

value: testicular germ cell tumor

value: 10 nM PFOS


title: IS-caput, Ovch2 KO, rep1


title: DMSO_P1_B02, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: IS-caput, Ovch2 KO, rep2


title: MeRIP (C4-2B dataset) T24R2 Rep 2 Input

value: cell line

value: MDVR

value: WT


title: MeRIP (C4-2B dataset) T24R2 Rep 1 Input

value: Human prostate cancer


title: DMSO_P1_B03, scRRBS (multi-omics)

value: No


title: BM_HSC_wt, rep3

value: wild-type

value: female


title: MeRIP C4-2B Rep 3 RIP

value: anti m6A antibody (NEB, E1610)

value: Day 3


title: RIP-seq_Treatment3

city: Shanghai

first: Ye

last: Zhou

address: Xiangyin Road

department: National Key Laboratory of Immunity & Inflammation

institute: Naval Medical University

data_processing:
The RNA fragments were incubated with the bead-linked FLAG antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 (v2.0.4). Methylated genes in each sample were then identified using MACS (1.4.2). Differential methylation gene identificationwas performed using diffReps (1.55.6). The peaks located mRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated gene.
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw counts for each sample

growth_protocol: DMEM, 10% fetal bocine serum, 1×penicilin/streptomycin. Cells were cultured at 37℃ with 5% CO2.

extract_protocol:
After treatment, the RNA fragments extrated from all the samples were incubated with the bead-linked FLAG antibodies and rotated at 4  C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction. The data of the six samples are IP, the data for input has not been uploaded.Total RNA was extracted using Trizol reagent
RNA libraries for IP samples were then constructed with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced in sequencer.

treatment_protocol: Cells are transfected with Flag-tagged-G3BP1 plasmid in all the samples. And the samples which are described as "Control" (C1, C2, C3), meaning the cells are not treated. The samples which are described as "Treatment"(H1, H2, H3), meaning the cells are treated with houst dust mite to induce SG assembly.

tag: rip antibody

value: anti-FLAG (Millipore, Cat# M8823)


title: DMSO_P1_B11, scRRBS (multi-omics)


title: DMSO_P1_B01, scRRBS (multi-omics)


title: DT D2

first: Jason

middle: C

last: Mills

address: 1 Baylor Plaza

department: Gastroenterology

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Quality control for filtering, normalization, clustering, and differential expression analysis was conducted in Seurat/R (Seurat  v4)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: gastric corpus epithelium

extract_protocol:
Fresh gastric corpus was harvested and mechanically dissociated in DMEM media+ Collagenase 1A while shaking at  37° for 30 minutes. Tissue was further dissociated chemically in 5-15 minutes at 37° in 0.05% trypsin-EDTA. The single cell suspension was passed through a 30µm filter, quantity and viability assessed with hematocytometer, and submitted to the Single Cell Genomics Core at Baylor College of Medicine in 0.04% BSA 1x PBS.
The single-cell gene expression Library was prepared according to the Chromium Single Cell Gene Expression 3’v3.1 instruction (PN-1000121, PN-1000120, PN-1000213, 10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS are broken and cDNA from each single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR.  The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification. After passed the quality control, the next-generation sequencing of libraries was performed on NovaSeq 6000 (Illumina).

treatment_protocol: Mice in experimental group were treated with diphtheria toxin (225ng/mouse) once a day for two days. Tissue was harvested at 24h after final injection. This timepoint contains three female mice

value: gastric corpus epithelium

value: Epithelium

value: Diphtheria-Toxin treated for 2 days


title: C1.PFOS_10.1

value: testes


title: DMSO_P1_A11, scRRBS (multi-omics)


title: RIP-seq_Treatment2


title: C1.DMSO.3

value: testicular germ cell tumor

value: control


title: MeRIP C4-2B Rep 2 RIP


title: MeRIP (C4-2B dataset) T24R2 Rep 3 Input

value: Input Ctrl - no antibody


title: C1.DMSO.2


title: RIP-seq_Treatment1


title: C1.PFOS_10.3

value: 10 nM PFOS


title: RIP-seq_Control3


title: DMSO_P1_A08, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: C1.PFOS_10.2


title: DMSO_P1_A12, scRRBS (multi-omics)


title: RIP-seq_Control2


title: C1.DMSO.1


title: MeRIP C4-2B Rep 1 RIP

value: cell line

value: WT


title: DMSO_P1_A07, scRRBS (multi-omics)

value: No


title: MeRIP C4-2B Rep 3 Input

value: Human prostate cancer


title: EP.5uMPFOS.2

value: EP

value: 5 uM PFOS


title: MeRIP C4-2B Rep 4 RIP

value: anti m6A antibody (NEB, E1610)

value: Day 3


title: DMSO_P1_B09, scRRBS (multi-omics)


title: MeRIP C4-2B Rep 4 Input


title: RIP-seq_Control1

value: anti-FLAG (Millipore, Cat# M8823)


title: EP.5uMPFOS.1


title: RNA-seq_KO2

data_processing:
The  RNA is purified by phenol:chloroform extraction.
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05)
Assembly: mm39
Supplementary files format and content: tab-delimited with raw counts and FPKM

source_name: macrophage

extract_protocol:
Total RNA was extracted using Trizol reagent
Total RNA was extracted followed by library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ). Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000. The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).

value: macrophage


title: EP.10nMPFOS.2


title: DMSO_P1_B10, scRRBS (multi-omics)


title: MeRIP C4-2B Rep 1 Input


title: EP.10nMPFOS.1


title: DMSO_P1_A04, scRRBS (multi-omics)


title: RNA-seq_WT2


title: EP.DMSO.2


title: RNA-seq_WT1


title: C1.DMSO.4


title: EP.DMSO.1


title: DMSO_P1_B08, scRRBS (multi-omics)


title: E-lncA411-78h

first: Yi

last: Feng

address: Jingxiu Road, Panyu District

institute: the First Affiliated Hospital of Guangzhou Medical University

data_processing:
Construction of Illumina PE library
Initial quality assessment of sequencing reads using FastQC
Quality cutting and statistics of sequencing data
Compare with reference genome using GRCh38 (ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/ )
Gene coverage analysis using HISAT and StringTie softwares
Assembly: Gene expression analysis using StringTie software
Supplementary files format and content: tab-delimited text files include count for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: peripheral blood

extract_protocol:
1. Exosome isolation. The exosomes was isolated by SEC (size exclution chromatography) methods. Briefly, 1 mL of 0.8 μm-filtered blood plasma was 1.5-fold diluted with PBS and further purified using Exosupur® columns (Echobiotech, China). The samples were then eluted with further 0.1 M PBS and a total of 2 mL eluate fractions were collected according to the manufacturer’s instructions. Fractions were concentrated to 200 μL by 100 kDa molecular weight cut-off Amicon® Ultra spin filters (Merck, Germany). 2.Nanoparticle tracking analysis (NTA). Vesicle suspensions with concentrations between 1x107/ml and 1x109/ml were examined using the ZetaView PMX 110 (Particle Metrix, Meerbusch, Germany) equipped with a 405 nm laser to determine the size and quantity of particles isolated. A video of 60-sec duration was taken with a frame rate of 30 frames/sec, and particle movement was analyzed using NTA software (ZetaView 8.02.28). 3. Transmission electron microscopy (TEM). 10 µl exosomes solution was placed on a copper mesh and incubated at room temperature for 10 min. After washing with sterile distilled water, the exosome was contrasted by uranyl-oxalate solution for 1 min. The sample was then dried for 2 min under incandescent light. The copper mesh was observed and photographed under a transmission electron microscope (H-7650, Hitachi Ltd., Tokyo, Japan). 4. Western blot analysis. The exosome supernatant was denatured in 5× sodium dodecyl sulfonate (SDS) buffer and subjected to western blot analysis (10% SDS-polyacrylamide gel electrophoresis; 50 µg protein/lane) using rabbit polyclonal antibody CD63 (sc-5275, Santa Cruz, CA, USA), CD9 (60232-I-Ig, Proteintech, Rosemont, IL), HSP90 (60318-I-Ig, Proteintech, Rosemont, IL), Alix (sc-53540, Santa Cruz, CA, USA), TSG101 (sc-13611, Santa Cruz, CA, USA) and calnexin (10427-2-AP, Promega, Madison, WI). The proteins were visualized on the Tanon4600 Automatic chemiluminescence image analysis system (Tanon, Shanghai, China). 5. ExoRNA isolation and RNA analyses. Total RNA was extracted and purified from plasma exosome using miRNeasy® Mini kit (Qiagen, cat. No. 217004) according to the kit instruction. RNA concentration and purity were evaluated using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA). The total RNA from exosomes was extracted using miRNeasy® Mini kit (Qiagen, cat. No. 217004) according to the manufacturer’s protocol. The total RNA was then reverse transcribed to synthesize cDNA using PrimeScript™ RT reagent Kit (Perfect Real Time) (TAKARA, RR037A).
RNA libraries were prepared for sequencing using standard Illumin protocol

treatment_protocol: After baseline information collection, patients received intravenous drip sintilimab 200 mg per 3 weeks for 4 cycles; blood sampling before every cycle and chest CT scan after every 2 cycles.

value: peripheral blood

tag: disease

value: early-stage lung cancer

tag: agent

value: sintilimab

tag: group

value: Non-responsed to sintilimab


title: DMSO_P1_B07, scRRBS (multi-omics)


title: DMSO_P1_A02, scRRBS (multi-omics)


title: RKIP KO1

city: Hangzhou

first: Fengdong

last: Zhao

state: Zhejiang

address: No. 3, Qingchun Road East

institute: Sir Run Run Shaw Hospital, Zhejiang University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Solanum lycopersicum（https://solgenomics.net/ftp/genomes/Solanum_lycopersicum/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: MSU_V7.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: bone marrow

value: primary cell

tag: cell type

value: bone marrow macrophages

value: RKIP KO

value: Macrophage-Colony Stimulating Factor (M-CSF) treatment


title: RKIP KO3


title: RKIP KO2


title: DMSO_P1_B06, scRRBS (multi-omics)

first: Masashi

last: Nomura

address: 149 13th street

institute: Massachusetts General Hospital

source_name: Mouse cell line single cell, IDHmutant mouse glioma cell

value: No


title: E-lncA411-69h


title: RKIP WT3

value: WT


title: DMSO_P1_A06, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: E-lncA411-77h


title: MeRIP C4-2B Rep 2 Input

value: cell line

value: Human prostate cancer

value: Input Ctrl - no antibody


title: DMSO_P1_H05, scRRBS (multi-omics)


title: E-lncA411-68h


title: RKIP WT2


title: DMSO_P1_A05, scRRBS (multi-omics)


title: RNA-seq_KO1


title: RKIP WT1


title: DMSO_P1_H04, scRRBS (multi-omics)


title: iPSCMG_TFS_HIV_BaL_d8_biol_rep3

city: Cincinnati

last: Hammonds

state: Ohio

address: 3333 Burnet Ave

department: Infectious Diseases

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw reads from purified RNA of cultured macrophages/microglia were processed using the nf-core/rnaseq pipeline version 3.4
Adapter sequences and low-quality reads were filtered and trimmed using FastQ and Trim Galore. Filtered reads were mapped to the human GRCh38 reference genome version 108 using STAR
Duplicate reads were removed using MarkDuplicates. Next, Salmon [10.1038/nmeth.4197] was used to generate a count matrix from genes with mapped reads.
Assembly: hg38
Supplementary files format and content: Transcripts counts table text file
Supplementary files format and content: tab-delimited text file includes raw counts for each sample to include those present in principle component analysis of Figure 1A.
Supplementary files format and content: tab-delimited text file included raw counts for each sample
Supplementary files format and content: tab-delimited text file includes metadata for each sample

source_name: cord blood-derived CD34+ progenitors

growth_protocol: Detailed methods for isolation, maturation and maintenance of human iMGLs provided in Stem Cell-derived Microglia Exhibit HAND Gene Expression Signature Immediately Upon Infection with HIV-1.

extract_protocol:
Total cellular RNA was extracted from 1 x10^6 iMGLs using QIAGEN RNeasy Mini Kit following standard operating procedures.
For high through-put RNA sequencing, 300 ng of RNA per sample was used to construct RNAseq libraries employing Illumina TruSeq mRNA standard protocols.

treatment_protocol: Infection with primary HIV-1 isolate BaL at an MOI of 0.25.

value: cord blood-derived CD34+ progenitors

value: iMGL

value: Female

value: Day 8

value: HIV-1 BaL Infected


title: DMSO_P1_H03, scRRBS (multi-omics)


title: iPSCMG_TFS_HIV_BaL_d8_biol_rep2


title: DMSO_P1_H01, scRRBS (multi-omics)


title: E-lncA411-60h

value: peripheral blood

value: early-stage lung cancer

value: sintilimab

value: Responsed to sintilimab


title: Liver innate immune cells, HTO-derived cDNA, lane 1

city: Hachioji

first: Kenichi

last: Asano

state: Tokyo

address: 1432-1 Horinouchi

department: Life Sciences

institute: Tokyo University of Pharmacy and Life Sciences

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

data_processing:
A951, A952,A953 and A964 datasets were integrated with merge functions of Seurat (version 4.1.1 in R version 4.2.1.).
Cells that contained more than 25% of mitochondrial transcripts were filtered out.
PCA analysis was performed against 5054 of highly-variable genes identified by FindVariableFeatures (selection.method = mvp, mean.cutoff = c(0.1, Inf), dispersion.cutoff = c(0.5, Inf)) function in Seurat.
1:57 PCs were selected by Jackstraw analysis and used for clustering analysis.
UMAP was performed on significant PCs for visualization in two dimensions.
Assembly: GRCm38 release 101
Supplementary files format and content: gene-expression matrix (.txt.gz)

molecule: protein

source_name: Liver

extract_protocol:
Liver innate immune cells from ND-fed or CDA-HFD-fed WT and EGR2-KO mice were sorted by FACSAriaIII and stained with different DNA barcode-conjugated PE-streptavidins (BioLegend Totalseq PE-streptavidin (A951, A952, A953, and A954)) to identify each sample origin.
Sorted cells were pooled and subject to scRNA-seq using BD RhapsodyTM Single-Cell Analysis System (BD  Biosciences), and resultant cDNA was amplified by TAS-Seq protocol. 3,000 cells /A951 ; 3,000 cells /A952 ; 9,000 cells /A953 ; 9,000 cells /A964 were loaded onto BD RhapsodyTM Single-Cell Analysis System.
cDNA library was processed into a sequencing library by using an NEBNext Ultra II FS DNA library prep kit for Illumina (New England Biolabs).
Sequencing adapters were added to associated Totalseq PE-streptavidin libraries by PCR.
Pooled library concentration was adjusted to 2.0 nM and 12% PhiX control library v3 (Illumina) was spiked into the library.

value: Liver

value: CD45.2+Lin (CD90.2, B220, NK1.1, SiglecF)-CD11b+ liver innate immune cells

value: Egr2fl/fl or Lyz2Cre/+.Egr2fl/fl

value: Normal diet or CDA-HFD

tag: library type

value: HTO

tag: antibodies/tags

value: Liver innate immune cells from ND-fed Egr2fl/fl mouse/TotalSeq-A951; Liver innate immune cells from ND-fed Lyz2Cre/+.Egr2fl/fl/TotalSeq-A952; Liver innate immune cells from CDA-HFD-fed Egr2fl/fl/TotalSeq-A953; Liver innate immune cells from CDA-HFD-fed Lyz2Cre/+.Egr2fl/fl /TotalSeq-A954


title: Liver innate immune cells, mRNA-derived cDNA, lane 1

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
cell names in processed files are as follows: [HTO ID]_[DataID]_[Cell barcode number]

tag: treatment

value: mRNA


title: iPSCMG_TFS_HIV_BaL_d8_biol_rep1

tag: cell line


title: E-lncA411-76h

value: Non-responsed to sintilimab


title: DMSO_P1_G12, scRRBS (multi-omics)

city: Charlestown

value: Mouse cell line single cell, IDHmutant mouse glioma cell

value: No


title: S1.IP

data_processing:
RNA was decapping with Decapping Enzyme,and then randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m7G antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 (v2.0.4). Methylated genes in each sample were then identified using MACS (1.4.2). Differential methylation gene identificationwas performed using diffReps (1.55.6). The peaks located mRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated gene.
Assembly: mm39
Supplementary files format and content: tab with methylated RNA sites and Peak (except for Input sample)

extract_protocol:
Total RNA was extracted using Trizol reagent
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced in sequencer.

treatment_protocol:
Previous studies already showed that stressed RNA granule pellet could be a reasonable proxy for full SG preparation,[1] thus we used SG core enriched fraction to validate the enriched transcripts.After House dust mite treatment for 30min, one 15 cm-dish cells were washed twice with ice-cold PBS quickly (within 10s) and then harvested in 1.5 ml ice-cold SG lysis buffer (50mM Tris pH 7.6, 50mM NaCl, 5mM MgCl2,0.1% NP-40, 1mM b-mercaptoethanol, 1% EDTA-free protease inhibitor cocktail, and 0.4 U/mL RNase inhibitor) on ice for 20 min. After that, cell suspensions were given 30 strokes in a Dounce homogenizer. 1/10 of cell suspensions were  separated as total cell fractions. The other cell suspensions was centrifuged at 2,000 g for 5 min at 4  . The supernatant contains cytosolic fraction, and the pellet contains nuclear fraction. Then, 1 ml of the supernatant was centrifuged at 18,000 g for 20 min at 4   to isolate the insoluble pellet fraction. After discarding the supernatant, the pellet was re-suspended in 1 ml lysis buffer and centrifuged at 18,000 g for another 20 min at 4  . Then, the supernatant was discarded, whereas the pellet was re-suspended in 300 ml SG lysis buffer and centrifuged at 850 g for 2 min at 4  . The supernatant represented SG core enriched fractions. The RNAs from total cell fractions, and SG core-enriched fractions were extracted using QIAzol (79306, Qiagen).
reference: 1. QKI shuttles internal m7G-modified transcripts into stress granules and modulates mRNA metabolism. Zhao et al., 2023, Cell 186, 1 C19.

value: anti-m7G (MBL International Corporation, Cat# RN017M)


title: iPSCMG_TFS_HIV_BaL_d6_biol_rep3

value: cord blood-derived CD34+ progenitors

value: iMGL

tag: Sex

value: Female

value: Day 6


title: E-lncA411-54h

value: peripheral blood

value: early-stage lung cancer

value: sintilimab


title: S1.Input

value: none (input)


title: DMSO_P1_H11, scRRBS (multi-omics)


title: iPSCMG_TFS_HIV_BaL_d6_biol_rep1

value: HIV-1 BaL Infected


title: iPSCMG_TFS_HIV_BaL_d6_biol_rep2


title: SG RNA3

data_processing:
The  RNA is purified by phenol:chloroform extraction.
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05)
Assembly: mm39
Supplementary files format and content: tab-delimited with raw counts

value: macrophage

tag: rna fraction

value: SG-associated RNA


title: E-lncA411-46h


title: DMSO_P1_G11, scRRBS (multi-omics)


title: DMSO_P1_H10, scRRBS (multi-omics)


title: E-lncA411-56h

value: Responsed to sintilimab


title: iPSCMG_TFS_HIV_BaL_d4_biol_rep3

tag: time

value: Day 4


title: E-lncA411-65h

tag: tissue

value: Non-responsed to sintilimab


title: DMSO_P1_G10, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell

tag: treatment (idhi)


title: E-lncA411-47h


title: E-lncA411-45h


title: iPSCMG_TFS_HIV_BaL_d4_biol_rep2


title: SG RNA1


title: SG RNA2


title: Total RNA3

value: total RNA


title: DMSO_P1_G09, scRRBS (multi-omics)

value: No


title: iPSCMG_TFS_HIV_BaL_d4_biol_rep1

value: cord blood-derived CD34+ progenitors


title: E-lncA411-44h


title: E-lncA411-43h


title: DMSO_P1_G08, scRRBS (multi-omics)


title: iPSCMG_TFS_HIV_BaL_d2_biol_rep3

value: iMGL

value: Day 2


title: Total RNA2


title: DMSO_P1_A03, scRRBS (multi-omics)


title: iPSCMG_TFS_HIV_BaL_d2_biol_rep2

value: Female


title: E-lncA411-37h

value: peripheral blood


title: E-lncA411-40h

value: early-stage lung cancer


title: Mouse_E14.5_Pinna_GFP

first: Xu

last: Xiaopeng

address: 96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District

institute: Guangzhou National Laboratory

data_processing:
The scRNA-seq reads were processed using the CeleScope pipeline, details of which are available at https://github.com/singleron-RD/CeleScope. This processing generated a 10x Genomics-like raw feature-barcode matrix suitable for downstream filtering and data integration using Seurat (version 4.3.0). For cell filtering, we assumed that both the log10-transformed gene counts and UMI counts per cell for each sample followed a normal distribution. We calculated the mean ± 1.96 times the standard deviation, defining the 95% confidence interval, to determine the lower and upper thresholds. These thresholds were then converted back to the original scale (as the power of 10 of the log values) to establish criteria for excluding low-quality cells. Furthermore, cells exhibiting a mitochondrial gene expression ratio exceeding 5% were also categorized as low quality.
Data integration was accomplished using the CCA2-based pipeline of Seurat package. The SelectIntegrationFeatures function was utilized to identify variable features across datasets for integration. Subsequently, the FindIntegrationAnchors function was employed to identify anchor pairs between datasets, followed by the IntegrateData function to create an integrated assay, which included the newly integrated expression profiles. Based on the results of integration, we performed PCA dimensionality reduction using RunPCA on the variable features employed for integration. This was followed by UMAP dimensionality reduction using RunUMAP with parameters -dims 1:20, -n.neighbors 50. For unsupervised clustering, we executed the FindNeighbors function using default parameters, and FindClusters with -resolution 0.4.
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: pinna

extract_protocol:
Micro-dissected forming pinna prominences from Hmx1wt/EGFP embryos were enzymatically dissociated using 0.5% trypsin/1× EDTA for 10 minutes at 37 °C (for E10.5 and E12.5 stages) and papain digestion mix for 7 minutes (for E14.5 stage). The treated tissues were then rinsed in ice-cold 1× DMEM, filtered, and GFP+ cells were enriched using FACS (Sony, MA900). These collected cells were resuspended and diluted in 1× DPBS (Cytiva) to a concentration of 1×106 cells per ml
Gene expression libraries were prepared using GEXSCOPE Single Cell RNA Library Kits v.2 (Singleron, catalog no. SD-4180022). The single-cell suspensions were loaded onto the GEXSCOPE microchip, which facilitates automated single cell capture, cell lysis, cellular mRNA capture, and molecular labeling via the Singleron Matrix instrument. The barcoded cDNA was amplified and utilized for constructing single cell NGS libraries. The quality and quantity of the resulting libraries were assessed using Qubit 4.0 (Thermo Fisher Scientific) and Qseq100 (Bioptic)

value: pinna


title: DMSO_P1_G07, scRRBS (multi-omics)


title: E-lncA411-38h

value: sintilimab


title: iPSCMG_TFS_HIV_BaL_d2_biol_rep1

value: HIV-1 BaL Infected


title: DMSO_P1_G06, scRRBS (multi-omics)


title: Mouse_E10.5_PA2_GFP

source_name: pharygneal arch 2

value: pharygneal arch 2


title: E-lncA411-36h


title: Mouse_E12.5_Pinna_GFP


title: E-lncA411-42h


title: DMSO_P1_H08, scRRBS (multi-omics)


title: iPSCMG_TFS_HIV_BaL_d1_biol_rep1

value: Day 1


title: iPSCMG_TFS_HIV_BaL_d1_biol_rep2


title: iPSCMG_TFS_HIV_BaL_d1_biol_rep3


title: E-lncA411-34h


title: Mouse_WT_E14.5_Pinna_rep4

data_processing:
RNA sequencing reads were initially processed using fastp for trimming of the paired-end data, with quality assessment performed via FASTQC. Subsequently, the reads were aligned to the mouse reference genome (GRCm39) using the STAR aligner. Quantification of the alignment files was carried out using featureCounts, incorporating the gene model parameter. Differential gene expression analysis was conducted utilizing the limma, Glimma, and edgeR packages
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Forming pinna prominences from E14.5 embryos (both wild type and mEC1dup/dup) were microdissected, washed with cold 1× PBS, and homogenized using a Tissue-Tearor. RNA extraction was performed according to the manufacturer’s protocol (RNeasy Mini Kit, Qiagen, 74104).
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

tag: genotype

value: Wild type (WT)


title: DMSO_P1_G04, scRRBS (multi-omics)


title: Mouse_WT_E14.5_Pinna_rep3


title: iPSCMG_TFS_HIV_BaL_d0_biol_rep2

value: Day 0

value: Uninfected


title: E-lncA411-32h

value: Non-responsed to sintilimab


title: DMSO_P1_H09, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: Total RNA1

value: macrophage

value: total RNA


title: Mouse_WT_E14.5_Pinna_rep2


title: Mouse_WT_E14.5_Pinna_rep5


title: iPSCMG_TFS_HIV_BaL_d0_biol_rep3

value: cord blood-derived CD34+ progenitors

value: iMGL


title: DMSO_P1_H07, scRRBS (multi-omics)

value: No


title: E-lncA411-35h

value: peripheral blood


title: E-lncA411-31h

value: early-stage lung cancer


title: DMSO_P1_G01, scRRBS (multi-omics)


title: Mouse_WT_E14.5_Pinna_rep1

value: pinna


title: E-lncA411-30h

value: sintilimab


title: iPSCMG_TFS_Uninfected_d8

value: Female

value: Day 8


title: DMSO_P1_G03, scRRBS (multi-omics)


title: iPSCMG_TFS_Uninfected_d6

value: Day 6


title: E-lncA411-29h


title: iPSCMG_TFS_HIV_BaL_d0_biol_rep1


title: DMSO_P1_F12, scRRBS (multi-omics)


title: Mouse_KI_E14.5_Pinna_rep4

value: Knock-In (KI)


title: Mouse_KI_E14.5_Pinna_rep5


title: DMSO_P1_F05, scRRBS (multi-omics)


title: iPSCMG_TFS_Uninfected_d4

value: Day 4


title: Mouse_KI_E14.5_Pinna_rep2


title: E-lncA411-28h


title: E-lncA411-27h


title: E-lncA411-26h

value: Responsed to sintilimab


title: DMSO_P1_F04, scRRBS (multi-omics)


title: DMSO_P1_F03, scRRBS (multi-omics)


title: Mouse_KI_E14.5_Pinna_rep1


title: iPSCMG_TFS_Uninfected_d1

value: Day 1

value: Uninfected


title: DMSO_P1_F02, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: E-lncA411-24h


title: Placental labyrinth zone Ctrl_M_4126_12

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Sample 24

data_processing:
STAR 2.5.0a was used to aligned the sequencing reads to the Mouse genome, and to perform gene-level counts using Ensembl gene model Version 100
Assembly: GRCm38
Supplementary files format and content: raw_counts.tsv
Supplementary files format and content: tab-delimited text with gene-level count

source_name: Placental labyrinth zone

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, UK) according to manufacturer’s protocol.
RNA-seq libraries were prepared from 500ng of RNA using TruSeq stranded total RNA library preparation kit (Illumina) and barcoded libraries were combined and submitted for sequencing (paired-end 50 cycles on a HiSeq6000) by the Wellcome Trust-MRC institute of Metabolic Science Genomics Core Facility.

value: Placental labyrinth zone

value: Male

value: Control diet


title: iPSCMG_72.3_HIV_BaL_d8_biol_rep3

source_name: Foreskin fibroblasts (FFs)

value: Foreskin fibroblasts (FFs)

value: HIV-1 BaL Infected


title: DMSO_P1_E12, scRRBS (multi-omics)

value: No


title: DMSO_P1_G02, scRRBS (multi-omics)


title: iPSCMG_72.3_HIV_BaL_d8_biol_rep2


title: iPSCMG_72.3_HIV_BaL_d8_biol_rep1


title: Placental labyrinth zone HFHS_M_4140_11

description: Sample 22

value: High fat high sugar diet


title: E-lncA411-23h

value: peripheral blood

value: early-stage lung cancer

value: sintilimab


title: Placental labyrinth zone HFHS_M_4177_12

description: Sample 23


title: DMSO_P1_F11, scRRBS (multi-omics)


title: Mouse_KI_E14.5_Pinna_rep3

value: pinna


title: iPSCMG_TFS_Uninfected_d2

value: cord blood-derived CD34+ progenitors

value: iMGL

value: Female

value: Day 2


title: E-lncA411-22h

value: Responsed to sintilimab


title: iPSCMG_72.3_HIV_BaL_d6_biol_rep2

value: Day 6


title: iPSCMG_72.3_HIV_BaL_d6_biol_rep3


title: E-lncA411-21h


title: Placental labyrinth zone HFHS_M_4073_10

description: Sample 21

value: Placental labyrinth zone


title: DMSO_P1_F10, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: E-lncA411-20h


title: Placental labyrinth zone HFHS_M_4068_09

description: Sample 20

value: Male


title: DMSO_P1_E09, scRRBS (multi-omics)


title: DMSO_P1_E07, scRRBS (multi-omics)


title: iPSCMG_72.3_HIV_BaL_d6_biol_rep1

value: Foreskin fibroblasts (FFs)


title: Placental labyrinth zone HFHS_M_4062_08

description: Sample 19


title: E-lncA411-18h


title: E-lncA411-19h


title: DMSO_P1_E06, scRRBS (multi-omics)


title: Placental labyrinth zone HFHS_M_3996_07

description: Sample 18


title: iPSCMG_72.3_HIV_BaL_d4_biol_rep2

value: Day 4

value: HIV-1 BaL Infected


title: E-lncA411-17h


title: DMSO_P1_F09, scRRBS (multi-omics)

value: No


title: Placental labyrinth zone HFHS_F_4177_06

description: Sample 17

value: High fat high sugar diet


title: DMSO_P1_E05, scRRBS (multi-omics)


title: iPSCMG_72.3_HIV_BaL_d4_biol_rep1


title: Placental labyrinth zone HFHS_F_4140_05

description: Sample 16


title: E-lncA411-16h

value: peripheral blood

value: early-stage lung cancer


title: iPSCMG_72.3_HIV_BaL_d2_biol_rep3


title: Placental labyrinth zone HFHS_F_4073_04

description: Sample 15


title: iPSCMG_72.3_HIV_BaL_d2_biol_rep2


title: iPSCMG_72.3_HIV_BaL_d4_biol_rep3


title: E-lncA411-15h

value: sintilimab


title: E-lncA411-13h


title: DMSO_P1_E03, scRRBS (multi-omics)


title: DMSO_P1_E02, scRRBS (multi-omics)


title: DMSO_P1_F07, scRRBS (multi-omics)


title: iPSCMG_72.3_HIV_BaL_d2_biol_rep1


title: E-lncA411-12h


title: Placental labyrinth zone HFHS_F_4068_03

description: Sample 14


title: Placental labyrinth zone HFHS_F_3996_01

description: Sample 12


title: DMSO_P1_F06, scRRBS (multi-omics)


title: Placental labyrinth zone HFHS_F_4062_02

description: Sample 13


title: iPSCMG_72.3_HIV_BaL_d1_biol_rep3

value: Day 1


title: iPSCMG_72.3_HIV_BaL_d1_biol_rep1


title: E-lncA411-10h


title: iPSCMG_72.3_HIV_BaL_d1_biol_rep2


title: DMSO_P1_E01, scRRBS (multi-omics)


title: Placental labyrinth zone Ctrl_M_4061_10

description: Sample 10

value: Control diet


title: E-lncA411-11h


title: DMSO_P1_D12, scRRBS (multi-omics)


title: iPSCMG_72.3_HIV_BaL_d0_biol_rep3

value: Day 0

value: Uninfected


title: E-lncA411-08h

value: Responsed to sintilimab


title: DMSO_P1_F08, scRRBS (multi-omics)


title: E-lncA411-14h


title: Placental labyrinth zone Ctrl_M_4091_09

description: Sample 9


title: Placental labyrinth zone Ctrl_M_4085_08

description: Sample 8


title: DMSO_P1_D02, scRRBS (multi-omics)


title: E-lncA411-06h


title: iPSCMG_72.3_HIV_BaL_d0_biol_rep1


title: iPSCMG_72.3_HIV_BaL_d0_biol_rep2


title: Placental labyrinth zone Ctrl_M_4154_11

description: Sample 11


title: DMSO_P1_C12, scRRBS (multi-omics)


title: DMSO_P1_D03, scRRBS (multi-omics)


title: E-lncA411-03h


title: E-lncA411-01h


title: iPSCMG_72.3_Uninfected_d6

value: Day 6


title: Placental labyrinth zone Ctrl_F_4154_06

description: Sample 6

value: Placental labyrinth zone

value: Female


title: E-lncA411-05h


title: DMSO_P1_C08, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: Placental labyrinth zone Ctrl_M_4075_07

description: Sample 7

value: Male


title: DMSO_P1_D01, scRRBS (multi-omics)


title: E-lncA411-04h


title: iPSCMG_72.3_Uninfected_d2

value: Foreskin fibroblasts (FFs)

value: Day 2


title: DMSO_P1_C07, scRRBS (multi-omics)

value: No


title: iPSCMG_72.3_Uninfected_d4

value: Day 4


title: E-lncA411-02h

value: peripheral blood


title: iPSCMG_72.3_Uninfected_d8

value: Day 8


title: Lx761c-Sim3

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

institute: MSKCC

data_processing:
In-line UMI sequences were trimmed from the sequencing reads with Marianas (https://github.com/mskcc/Marianas) and aligned to human GRCh38 genome using STAR 2.7.0 (https://github.com/alexdobin/STAR) [25] with Ensembl v92 gene annotation.
Hybrid selection-specific metrics and alignment metrics were calculated for the BAM files using CalculateHsMetrics and CollectRnaSeqMetrics, respectively, from Picard Toolkit (https://github.com/broadinstitute/picard) to determine the quality of the capture.
We quantified RNA-seq reads with Kallisto v.0.45.053 to obtain transcript counts and abundances.
Transcript per million (TPM) normalization by size factors was done from Kallisto output files using Sleuth v0.30.0 run in gene mode.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with TPM values over all genes for each sample.

source_name: :Lung

extract_protocol:
Frozen tissues were weighed and homogenized in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN, #80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water.
Fresh cell pellet or frozen tumor samples were shipped to GENEWIZ for RNA isolation, library preparation, and RNA sequencing. Total RNA was extracted using the RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). RNA samples and sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). Sequencing libraries were clustered on one flowcell lane and then loaded on the Illumina HiSeq instrument (4000 or equivalent) (RRID: SCR_020127) according to manufacturer’s instructions. Samples were sequenced using a 2x150bp paired end (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bclfiles) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software (RRID: SCR_015058). One mismatch was allowed for index sequence identification.

value: :Lung

value: SCLC

value: Simurosertib


title: Placental labyrinth zone Ctrl_F_4061_04

description: Sample 4

value: Control diet


title: Placental labyrinth zone Ctrl_F_4085_02

description: Sample 2


title: DMSO_P1_D10, scRRBS (multi-omics)


title: DMSO_P1_D09, scRRBS (multi-omics)


title: Placental labyrinth zone Ctrl_F_4126_05

description: Sample 5


title: Lx761c-Sim2


title: MDM_HIV_BaL_d8_biol_rep3

source_name: Whole blood

value: Whole blood

value: Peripheral blood monocytes (PBMs)

value: Monocyte-derived macrophages (MDMs)

value: HIV-1 BaL Infected


title: Placental labyrinth zone Ctrl_F_4075_01

description: Sample 1

value: Placental labyrinth zone

value: Female


title: Placental labyrinth zone Ctrl_F_4091_03

description: Sample 3


title: Lx761c-Irino2

value: Irinotecan


title: DMSO_P1_C06, scRRBS (multi-omics)

value: Mouse cell line single cell, IDHmutant mouse glioma cell


title: MDM_HIV_BaL_d8_biol_rep2


title: GEX library Lane 3

city: Munich

first: Bhavishya

last: Nelakuditi

address: Marchioninistraße 15, 81377 München

institute: LMU Klinikum

data_processing:
Sequencing reads were processed using the Cell Ranger software with the mm10 mouse reference genome index provided by 10X Genomics
This resulted in a count matrix for 16045 cells and 32285 genes. The count data were analyzed using Seurat
Assembly: mm10
Supplementary files format and content: The Rds object contains the processed seurat object used in the analysis.

source_name: Long bones (femurs, tibiae, humerus)

extract_protocol: see  Chromium Next GEM Single Cell 3’ reagent kit v3.1 (CG000206 Rev D) from 10X Genomics

value: Long bones (femurs, tibiae, humerus)

value: bone marrow cells


title: DMSO_P1_C05, scRRBS (multi-omics)

data_processing:
Analysis of single cell DNA methylation data was performed based on the methods detailed in Chaligne et al 2021. After demultiplexing, reads were mapped to the mm10 genome and cells with at least 25,000 CpG sites, 1 million reads and mapping efficiency greater than 30% were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: tsv

value: No


title: GEX library Lane 2


title: Lx761c-Irino1


title: DMSO_P1_D08, scRRBS (multi-omics)


title: MDM_HIV_BaL_d6_biol_rep3

value: Day 6


title: DMSO_P1_D07, scRRBS (multi-omics)


title: MDM_HIV_BaL_d8_biol_rep1

value: Day 8


title: MDM_HIV_BaL_d6_biol_rep2


title: Lx761c-Ctrl4

value: :Lung

value: Control


title: iPSCMG_72.3_Uninfected_d1

value: Foreskin fibroblasts (FFs)

value: Male

value: Day 1

value: Uninfected


title: Lx761c-Ctrl3

value: SCLC


title: Lx761c-Ctrl2


title: DMSO_P1_C01, scRRBS (multi-omics)


title: MDM_HIV_BaL_d6_biol_rep1

value: Whole blood

value: Peripheral blood monocytes (PBMs)

value: Monocyte-derived macrophages (MDMs)

value: HIV-1 BaL Infected


title: CS library Lane 3


title: CS library Lane 1


title: MDM_HIV_BaL_d4_biol_rep3

value: Day 4


title: GEX library Lane 1

value: Long bones (femurs, tibiae, humerus)


title: Lx761c-Ctrl1